R Notebook

data = read_csv("data.csv") %>% 
  filter(!`Case Number` %in% readxl::read_xlsx("C:\\Users\\jagvan\\OneDrive - South Australia Government\\Code\\exclusions_2021.xlsx")$`Case Number`) %>% 
  mutate(`Age Group` = factor(`Age Group`, levels = 
                                c("< 28 days", "1 to 11 months", "1 to 4 years", "5 to 9 years", "10 to 14 years", "15 to 17 years"))) %>% 
  left_join(read_csv("C:\\Users\\jagvan\\OneDrive - South Australia Government\\REDCap\\ICD-10\\icd-10-chapters.csv")[c("Chapter", "Name")], by = "Chapter")

disability = data %>% filter(`Disability Register` == "Yes") %>% 
  mutate("Infant with disability" = ifelse(`Age (years)` < 1, "Yes", "No"))

disability_long = pivot_longer(disability, 
                               cols = c(Autism:`Other disability`,`Infant with disability`),
                               names_to = "Disability_category",
                               values_to = "Yes_No") %>% 
  filter(Yes_No == "Yes")

yearly = disability_long %>%
  mutate(Disability_category = as.factor(Disability_category),
         Disability_category = reorder(Disability_category, Disability_category, FUN=length)) %>%
  group_by(`Year of Death`, Disability_category) %>% 
  tally()  

yearly_percentage = data %>% 
  group_by(`Year of Death`, `Disability Register`) %>% 
  tally() %>% 
  pivot_wider(id_cols = `Year of Death`, names_from = `Disability Register`, values_from = n) %>% 
  mutate(Total = Yes + No,
         Prop_disability = Yes/No)

chapter_age = disability %>% 
  mutate(Chapter = as.factor(Chapter)) %>% 
  group_by(`Age Group`, Chapter, Name) %>% 
  tally()

(figure2 <- plot_ly(chapter_age,
        type = "bar",
        x = ~`Age Group`,
        y = ~n,
        color = ~fct_rev(Chapter),
        hovertemplate = paste0("Chapter ", chapter_age$Chapter, ": ", chapter_age$Name, "\n",
                               "Deaths: ", chapter_age$n, "<extra></extra>")) %>% 
  layout(barmode = "stack",
         font = list(size = 14),
         xaxis = list(title = "Age group"),
         yaxis = list(title = "Deaths"),
         legend = list(title = list(text="ICD-10\nChapter",
                                    font=list(size=12)),
                       font=list(size = 12)))
)

saveWidget(partial_bundle(figure2), "figure2.html", selfcontained = T)